USAGE: extract_fastq_barcodes_from_header.py input_reads.fastq barcode_reads.fastq
gregcaporaso
/ bio450-python-pt4-translation.ipynb
Created Feb 16, 2021
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gregcaporaso
/ qiime-exercise.ipynb
Created Apr 5, 2016
Final assignment for BIO/CS 499/599 (Spring 2016)
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gregcaporaso
/ README.md
Created Nov 17, 2012
quick and dirty script to create a barcode read fastq file from a sequence read fastq file with barcodes in the headers
gregcaporaso
/ notes.md
Last active Mar 28, 2019
vsearch-based sequence dereplication through generation of a biom table
View notes.md
This depends on biom version >= 2.1.5, < 2.2.0 and vsearch >= 1.7.0.
Please note that all of this is highly experimental. I'm keeping these notes as I work with this approach. For published work, I still recommend using standard pipelines, such as those in QIIME 1.9.1.
$ biom --version
biom, version 2.1.5
$ vsearch --version
vsearch v1.7.0_osx_x86_64, 16.0GB RAM, 8 cores
gregcaporaso
/ neighbor-joining-experiments.ipynb
Created Jun 11, 2014
initial experiments with implementing neighbor joining for scikit-bio
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gregcaporaso
/ q2d3-test.ipynb
Created Mar 9, 2016
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gregcaporaso
/ artifact-demo.ipynb
Created Mar 8, 2016
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gregcaporaso
/ check_illumina_barcodes.py
Created Dec 3, 2013
Script for performing some basic testing on Illumina amplicon sequencing primers as described in: http://www.nature.com/ismej/journal/v6/n8/full/ismej20128a.html
View check_illumina_barcodes.py
| #!/usr/bin/env python | |
| # File created on 01 Dec 2011 | |
| from __future__ import division | |
| __author__ = "Greg Caporaso" | |
| __copyright__ = "Copyright 2011, The QIIME project" | |
| __credits__ = ["Greg Caporaso"] | |
| __license__ = "GPL" | |
| __version__ = "1.3.0-dev" | |
| __maintainer__ = "Greg Caporaso" |
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